Merge branch 'other/MITY-18-replace-mity-report' of github.com:KCCG/mity into feature/MITY-32-rewrite-commands-and-add-classes

Author: trentzz

docs/mity-report-annotations.md

@@ -0,0 +1,30 @@
+# mity report annotations
+
+## Adding new annotations
+
+1. Place annotations file (and index file) in `mitylib/annot`.
+2. Add a new vcfanno entry for the file in `vcfanno-config.toml`
+3. Add new fields in `annotations` and `excel_headers` in `report-config.yaml`.
+
+```yaml
+excel_headers:
+- SAMPLE
+- HGVS
+- GENE/LOCUS
+...
+- YOUR NEW EXCEL HEADER
+```
+
+Note that the order of headers in this yaml file represents the order of columns in the final excel file.
+
+```yaml
+vcf_headers:
+  annotations:
+    GenBank_frequency_mitomap: GENBANK FREQUENCY MITOMAP
+    MGRB_AC: MGRB AC
+    MGRB_AN: MGRB AN
+    ...
+    your_annotation_field_name: YOUR NEW EXCEL HEADER
+```
+
+Note that `your_annotation_field_name` needs to match the info field name exactly.

mitylib/report.py

@@ -1,5 +1,5 @@
 """
-TODO: Mity report description.
+Adds annotations and generates mity excel report from VCF file.
 """
 
 import logging
@@ -60,7 +60,9 @@ def find_highest_impact(self, impacts):
         if "LOW" in impacts:
             return "LOW"
 
-        raise ValueError("Unknown SO term.")
+        logging.warning("Unknown SO term.")
+
+        return ""
 
     def get_vep_values(self, variant):
         """
@@ -393,7 +395,7 @@ def make_table(self):
                 # that this is still valid.
                 if "Genbank_frequency_mitomap" in sample.keys():
                     allele_frequency_mitomap = round(
-                        float(sample["GenBank_frequency_mitomap"]) / 32050, 3
+                        float(sample["GenBank_frequency_mitomap"]) / 32059, 3
                     )
                 else:
                     allele_frequency_mitomap = "."